diff --git a/assembly.py b/assembly.py
index 62ae45729..4ac7d638b 100755
--- a/assembly.py
+++ b/assembly.py
@@ -97,7 +97,7 @@ def parser_trim_rmdup_subsamp(parser=argparse.ArgumentParser()):
 __commands__.append(('trim_rmdup_subsamp', parser_trim_rmdup_subsamp))
 
 
-def assemble_trinity(inBam, outFasta, clipDb, n_reads=100000, outReads=None):
+def assemble_trinity(inBam, outFasta, clipDb, n_reads=100000, outReads=None, JVMmemory=None):
     ''' This step runs the Trinity assembler.
         First trim reads with trimmomatic, rmdup with prinseq,
         and random subsample to no more than 100k reads.
@@ -110,7 +110,7 @@ def assemble_trinity(inBam, outFasta, clipDb, n_reads=100000, outReads=None):
     trim_rmdup_subsamp_reads(inBam, clipDb, subsamp_bam, n_reads=n_reads)
     subsampfq = list(map(util.file.mkstempfname, ['.subsamp.1.fastq', '.subsamp.2.fastq']))
     tools.picard.SamToFastqTool().execute(subsamp_bam, subsampfq[0], subsampfq[1])
-    tools.trinity.TrinityTool().execute(subsampfq[0], subsampfq[1], outFasta)
+    tools.trinity.TrinityTool().execute(subsampfq[0], subsampfq[1], outFasta, JVMmemory=JVMmemory)
     os.unlink(subsampfq[0])
     os.unlink(subsampfq[1])
     
@@ -128,6 +128,9 @@ def parser_assemble_trinity(parser=argparse.ArgumentParser()):
         help='Subsample reads to no more than this many pairs. (default %(default)s)')
     parser.add_argument('--outReads', default=None,
         help='Save the trimmomatic/prinseq/subsamp reads to a BAM file')
+    parser.add_argument('--JVMmemory',
+        default=tools.trinity.TrinityTool.jvmMemDefault,
+        help='JVM virtual memory size (default: %(default)s)')
     util.cmd.common_args(parser, (('loglevel',None), ('version',None), ('tmpDir',None)))
     util.cmd.attach_main(parser, assemble_trinity, split_args=True)
     return parser
diff --git a/docs/install.rst b/docs/install.rst
index 3639a51cd..50115454c 100644
--- a/docs/install.rst
+++ b/docs/install.rst
@@ -38,7 +38,7 @@ Additionally, in order to use the **pipeline infrastructure**, Python 3.4
 is required (Python 2 is not supported) and you must install snakemake
 as well::
 
-  pip install snakemake==3.2 yappi=0.94
+  pip install snakemake==3.2.1 yappi=0.94
 
 However, most of the real functionality is encapsulated in the command line
 tools, which can be used without any of the pipeline infrastructure.
diff --git a/pipes/Snakefile b/pipes/Snakefile
index 6c198aab5..167e9fab2 100644
--- a/pipes/Snakefile
+++ b/pipes/Snakefile
@@ -37,10 +37,7 @@ rule all:
         os.path.join(config["dataDir"], config["subdirs"]["interhost"], 'ref_guided.fasta'),
         os.path.join(config["dataDir"], config["subdirs"]["interhost"], 'ref_guided.vcf.gz'),
         # create summary reports
-        config["reportsDir"]+'/summary.coverage_ref.txt.gz',
-        config["reportsDir"]+'/summary.coverage_self.txt.gz',
         config["reportsDir"]+'/summary.fastqc.txt',
-        config["reportsDir"]+'/summary.bamstats.txt',
         config["reportsDir"]+'/summary.spike_count.txt'
     params: LSF="-N"
     run:
diff --git a/pipes/rules/assembly.rules b/pipes/rules/assembly.rules
index b56cf512d..7782d4dcc 100644
--- a/pipes/rules/assembly.rules
+++ b/pipes/rules/assembly.rules
@@ -19,10 +19,6 @@ rule all_assemble:
         # create BAMs of aligned reads to own consensus
         expand("{dataDir}/{subdir}/{sample}.bam",
             dataDir=config["dataDir"], subdir=config["subdirs"]["align_self"],
-            sample=read_samples_file(config["samples_assembly"])),
-        # assembly reports too
-        expand("{reportsDir}/assembly/{sample}.txt",
-            reportsDir=config["reportsDir"],
             sample=read_samples_file(config["samples_assembly"]))
     params: LSF="-N"
 
@@ -30,10 +26,7 @@ rule all_assemble_failures:
     input:
         expand("{dataDir}/{subdir}/{sample}.fasta",
             dataDir=config["dataDir"], subdir=config["subdirs"]["assembly"],
-            sample=read_samples_file(config.get("samples_assembly_failures"))),
-        expand("{reportsDir}/assembly/{sample}.txt",
-            reportsDir=config["reportsDir"],
-            sample=read_samples_file(config["samples_assembly"]))
+            sample=read_samples_file(config.get("samples_assembly_failures")))
     params: LSF="-N"
 
 
@@ -45,7 +38,7 @@ rule assemble_trinity:
     '''
     input:  config["dataDir"]+'/'+config["subdirs"]["per_sample"]+'/{sample}.taxfilt.bam'
     output: config["tmpDir"] +'/'+config["subdirs"]["assembly"]+'/{sample}.assembly1-trinity.fasta'
-    resources: mem=3
+    resources: mem=4
     params: LSF=config.get('LSF_queues', {}).get('short', '-W 4:00'),
             n_reads="100000",
             logid="{sample}",
@@ -80,8 +73,7 @@ rule orient_and_impute:
             multi-chromosome genomes.
     '''
     input:  config["tmpDir"]+'/'+config["subdirs"]["assembly"]+'/{sample}.assembly1-trinity.fasta'
-    output: config["tmpDir"]+'/'+config["subdirs"]["assembly"]+'/{sample}.assembly2-vfat.fasta',
-            config["tmpDir"]+'/'+config["subdirs"]["assembly"]+'/{sample}.assembly3-modify.fasta'
+    output: config["tmpDir"]+'/'+config["subdirs"]["assembly"]+'/{sample}.assembly3-modify.fasta'
     resources: mem=3
     params: LSF=config.get('LSF_queues', {}).get('short', '-W 4:00'),
             refGenome=config["ref_genome"],
@@ -90,10 +82,11 @@ rule orient_and_impute:
             renamed_prefix="",
             replace_length="55",
             logid="{sample}",
+            vfat_fasta=config["tmpDir"]+'/'+config["subdirs"]["assembly"]+'/{sample}.assembly2-vfat.fasta',
             subsamp_bam=config["tmpDir"]+'/'+config["subdirs"]["assembly"]+'/{sample}.subsamp.bam'
     run:
-            shell("{config[binDir]}/assembly.py order_and_orient {input} {params.refGenome} {output[0]} --inReads {params.subsamp_bam}")
-            shell("{config[binDir]}/assembly.py impute_from_reference {output[0]} {params.refGenome} {output[1]} --newName {params.renamed_prefix}{wildcards.sample} --replaceLength {params.replace_length} --minLength {params.length} --minUnambig {params.min_unambig}")
+            shell("{config[binDir]}/assembly.py order_and_orient {input} {params.refGenome} {params.vfat_fasta} --inReads {params.subsamp_bam}")
+            shell("{config[binDir]}/assembly.py impute_from_reference {params.vfat_fasta} {params.refGenome} {output} --newName {params.renamed_prefix}{wildcards.sample} --replaceLength {params.replace_length} --minLength {params.length} --minUnambig {params.min_unambig}")
 
 rule refine_assembly_1:
     ''' This a first pass refinement step where we take the VFAT assembly,
@@ -148,8 +141,7 @@ rule map_reads_to_self:
     input:  config["dataDir"]+'/'+config["subdirs"]["per_sample"]+'/{sample}.cleaned.bam',
             config["dataDir"]+'/'+config["subdirs"]["assembly"]+'/{sample}.fasta'
     output: config["dataDir"]+'/'+config["subdirs"]["align_self"]+'/{sample}.bam',
-            config["dataDir"]+'/'+config["subdirs"]["align_self"]+'/{sample}.mapped.bam',
-            config["reportsDir"]+'/assembly/{sample}.txt'
+            config["dataDir"]+'/'+config["subdirs"]["align_self"]+'/{sample}.mapped.bam'
     resources: mem=4
     params: LSF=config.get('LSF_queues', {}).get('short', '-W 4:00'),
             logid="{sample}",
@@ -158,4 +150,3 @@ rule map_reads_to_self:
             makedirs([os.path.join(config["dataDir"], config["subdirs"]["align_self"]),
                 os.path.join(config["reportsDir"], "assembly")])
             shell("{config[binDir]}/read_utils.py align_and_fix {input} --outBamAll {output[0]} --outBamFiltered {output[1]} --novoalign_options '{params.novoalign_options}'")
-            shell("{config[binDir]}/reports.py assembly_stats {wildcards.sample} {output[2]} --assembly_dir {config[dataDir]}/{config[subdirs][assembly]} --assembly_tmp {config[tmpDir]}/{config[subdirs][assembly]} --align_dir {config[dataDir]}/{config[subdirs][align_self]}")
diff --git a/pipes/rules/reports.rules b/pipes/rules/reports.rules
index a95455790..d4dd4dca3 100644
--- a/pipes/rules/reports.rules
+++ b/pipes/rules/reports.rules
@@ -10,78 +10,10 @@ import os, os.path, gzip, shutil
 
 rule all_reports:
     input:
-        config["reportsDir"]+'/summary.coverage_ref.txt.gz',
-        config["reportsDir"]+'/summary.coverage_self.txt.gz',
         config["reportsDir"]+'/summary.fastqc.txt',
-        config["reportsDir"]+'/summary.bamstats.txt',
         config["reportsDir"]+'/summary.spike_count.txt'
     params: LSF="-N"
 
-#-----------BAMSTATS-------------------
-
-def bamstats_input_file(wildcards):
-    adj = wildcards.adjective
-    if adj in ('raw', 'cleaned'):
-        subdir = "depletion"
-    else:
-        if adj.startswith('self_'):
-            subdir = "align_self"
-        elif adj.startswith('ref_'):
-            subdir = "align_ref"
-        else:
-            raise Exception()
-        if adj.endswith('_mapped') or adj.endswith('_rmdup') or adj.endswith('_realigned'):
-            adj = adj.split('_')[-1]
-        elif adj.endswith('_align'):
-            adj = None
-        else:
-            raise Exception()
-    if adj==None:
-        bamfile = wildcards.sample + '.bam'
-    else:
-        bamfile = '.'.join([wildcards.sample, adj, 'bam'])
-    return os.path.join(config["dataDir"], config["subdirs"][subdir], bamfile)
-
-rule bamstats_report:
-    input:  bamstats_input_file
-    output: config["reportsDir"]+'/bamstats/{sample}.{adjective}.txt'
-    params: LSF='-W 0:30 -sp 40',
-            logid="{sample}-{adjective}",
-            tmpf_report=config["reportsDir"]+'/bamstats/{sample}.{adjective}.tmp.txt'
-    run:
-            makedirs(config["reportsDir"]+'/bamstats')
-            shell("use BamTools; bamtools stats -insert -in {input} > {params.tmpf_report}")
-            out = []
-            out.append(['Sample', wildcards.sample])
-            out.append(['BAM', wildcards.adjective])
-            with open(params.tmpf_report, 'rt') as inf:
-                for line in inf:
-                    row = line.strip().split(':')
-                    if len(row)==2 and row[1]:
-                        k,v = [x.strip() for x in row]
-                        k = k.strip("'")
-                        mo = re.match(r'^(\d+)\s+\(\S+\)$', v)
-                        if mo:
-                            v = mo.group(1)
-                        out.append([k,v])
-            with open(output[0], 'wt') as outf:
-                for row in out:
-                    outf.write('\t'.join(row)+'\n')
-            os.unlink(params.tmpf_report)
-
-rule consolidate_bamstats:
-    input:
-            expand("{{dir}}/bamstats/{sample}.{adjective}.txt",
-                adjective=['raw','cleaned',
-                    'ref_align', 'ref_mapped', 'ref_rmdup', 'ref_realigned'],
-                sample=read_samples_file(config["samples_per_run"])) + \
-            expand("{{dir}}/bamstats/{sample}.{adjective}.txt",
-                adjective=['self_align', 'self_mapped', 'self_rmdup', 'self_realigned'],
-                sample=read_samples_file(config["samples_assembly"]))
-    output: '{dir}/summary.bamstats.txt'
-    params: logid="all"
-    shell:  "{config[binDir]}/reports.py consolidate_bamstats {input} {output}"
-
 
 #-----------FASTQC---------------------
 
@@ -106,46 +38,6 @@ rule consolidate_fastqc:
     params: logid="all"
     shell:  "{config[binDir]}/reports.py consolidate_fastqc {input} {output}"
 
-#-----------COVERAGE-------------------
-
-def coverage_input_files(wildcards):
-    if wildcards.adjective == 'ref':
-        ref   = config["ref_genome"]
-        reads = os.path.join(config["dataDir"], config["subdirs"]["align_ref"], wildcards.sample + '.realigned.bam')
-    elif wildcards.adjective == 'self':
-        ref   = os.path.join(config["dataDir"], config["subdirs"]["assembly"], wildcards.sample + '.fasta')
-        reads = os.path.join(config["dataDir"], config["subdirs"]["align_self"], wildcards.sample + '.realigned.bam')
-    else:
-        raise Exception()
-    return (ref, reads)
-
-rule coverage_report:
-    input:  coverage_input_files
-    output: config["reportsDir"]+'/coverage/{sample}.coverage_{adjective}.txt'
-    resources: mem=3
-    params: LSF=config.get('LSF_queues', {}).get('short', '-W 4:00') + " -sp 40",
-            logid="{sample}-{adjective}"
-    run:
-            makedirs(os.path.join(config["reportsDir"], 'coverage'))
-            shell("/idi/sabeti-scratch/kandersen/bin/bedtools/bedtools genomecov -d -ibam {input[1]} -g {input[0]} > {output}")
-
-def consolidate_coverage_inputs(wildcards):
-    if wildcards.adjective == 'ref':
-        samples = config['samples_per_run']
-    elif wildcards.adjective == 'self':
-        samples = config['samples_assembly']
-    else:
-        raise Exception()
-    return [wildcards.dir+'/coverage/'+sample+'.coverage_'+wildcards.adjective+'.txt'
-        for sample in read_samples_file(samples)]
-
-rule consolidate_coverage:
-    input:  consolidate_coverage_inputs
-    output: '{dir}/summary.coverage_{adjective}.txt.gz'
-    params: LSF=config.get('LSF_queues', {}).get('short', '-W 4:00'),
-            logid="all"
-    shell:  "{config[binDir]}/reports.py consolidate_coverage {input} {wildcards.adjective} {output}"
-
 
 #-----------SPIKE-INS------------------
 
@@ -171,5 +63,5 @@ rule consolidate_spike_count:
                 sample=read_samples_file(config["samples_per_run"]))
     output: '{dir}/summary.spike_count.txt'
     params: logid="all"
-    shell:  "{config[binDir]}/reports.py consolidate_spike_count {input} {output}"
+    shell:  "{config[binDir]}/reports.py consolidate_spike_count {wildcards.dir}/spike_count {output}"
 
diff --git a/pipes/rules/reports_only b/pipes/rules/reports_only
index 6e4997703..0d7b30e7e 100644
--- a/pipes/rules/reports_only
+++ b/pipes/rules/reports_only
@@ -52,5 +52,10 @@ rule assembly_report:
     resources: mem=2
     params: LSF=config.get('LSF_queues', {}).get('short', '-W 4:00'),
             logid="{sample}"
-    shell:  "{config[binDir]}/reports.py assembly_stats {wildcards.sample} {output} --assembly_dir {config[dataDir]}/{config[subdirs][assembly]} --assembly_tmp {config[tmpDir]}/{config[subdirs][assembly]} --align_dir {config[dataDir]}/{config[subdirs][align_self]}"
+    shell:  "{config[binDir]}/reports.py assembly_stats {wildcards.sample} {output}" \
+            " --assembly_dir {config[dataDir]}/{config[subdirs][assembly]}" \
+            " --assembly_tmp {config[tmpDir]}/{config[subdirs][assembly]}" \
+            " --align_dir {config[dataDir]}/{config[subdirs][align_self]}" \
+            " --reads_dir {config[dataDir]}/{config[subdirs][per_sample]}" \
+            " --raw_reads_dir {config[dataDir]}/{config[subdirs][source]}"
 
diff --git a/reports.py b/reports.py
index bb3b77e32..77129e525 100755
--- a/reports.py
+++ b/reports.py
@@ -23,16 +23,26 @@
 def get_assembly_stats(sample,
         cov_thresholds=(1,5,20,100),
         assembly_dir='data/02_assembly', assembly_tmp='tmp/02_assembly',
-        align_dir='data/02_align_to_self'):
+        align_dir='data/02_align_to_self', reads_dir='data/01_per_sample',
+        raw_reads_dir='data/00_raw'):
     ''' Fetch assembly-level statistics for a given sample '''
     out = {'sample':sample}
     samtools = tools.samtools.SamtoolsTool()
-    header = ['sample', 'assembled_trinity', 'trinity_in_reads',
+    header = ['sample', 'reads_raw', 'reads_cleaned', 'reads_taxfilt',
+        'assembled_trinity', 'trinity_in_reads',
         'n_contigs', 'contig_len', 'unambig_bases', 'pct_unambig',
         'aln2self_reads_tot', 'aln2self_reads_aln', 'aln2self_reads_rmdup', 'aln2self_pct_nondup',
         'aln2self_cov_median', 'aln2self_cov_mean', 'aln2self_cov_mean_non0',
         ] + ['aln2self_cov_%dX'%t for t in cov_thresholds]
     
+    # per-sample unaligned read stats
+    for adj in ('cleaned', 'taxfilt'):
+        reads_bam = os.path.join(reads_dir, '.'.join((sample, adj, 'bam')))
+        if os.path.isfile(reads_bam):
+            out['reads_'+adj] = samtools.count(reads_bam)
+    out['reads_raw'] = sum(samtools.count(bam)
+        for bam in glob.glob(os.path.join(raw_reads_dir, sample+"*.bam")))
+    
     # pre-assembly stats
     out['assembled_trinity'] = os.path.isfile(os.path.join(assembly_tmp,
         sample + '.assembly1-trinity.fasta')) and 1 or 0
@@ -43,11 +53,14 @@ def get_assembly_stats(sample,
     # assembly stats
     assembly_fname = os.path.join(assembly_dir, sample + '.fasta')
     if not os.path.isfile(assembly_fname):
-        out['n_contigs'] = 0
-        return (header, out)
+        assembly_fname = os.path.join(assembly_tmp, sample + '.assembly2-vfat.fasta')
+        if not os.path.isfile(assembly_fname):
+            out['n_contigs'] = 0
+            return (header, out)
     with open(assembly_fname, 'rt') as inf:
         counts = [(len(s), assembly.unambig_count(s.seq))
-            for s in Bio.SeqIO.parse(inf, 'fasta')]
+            for s in Bio.SeqIO.parse(inf, 'fasta')
+            if len(s)>0]
     out['n_contigs'] = len(counts)
     out['contig_len'] = ','.join(str(x) for x,y in counts)
     out['unambig_bases'] = ','.join(str(y) for x,y in counts)
@@ -76,13 +89,17 @@ def get_assembly_stats(sample,
     return (header, out)
 
 def assembly_stats(samples, outFile,
-    cov_thresholds, assembly_dir, assembly_tmp, align_dir):
+    cov_thresholds, assembly_dir, assembly_tmp, align_dir,
+    reads_dir, raw_reads_dir):
     ''' Fetch assembly-level statistics for a given sample '''
     header_written = False
     with open(outFile, 'wt') as outf:
         for sample in samples:
             log.info("fetching stats on "+sample)
-            header, out = get_assembly_stats(sample, cov_thresholds, assembly_dir, assembly_tmp, align_dir)
+            header, out = get_assembly_stats(sample,
+                cov_thresholds=cov_thresholds, assembly_dir=assembly_dir,
+                assembly_tmp=assembly_tmp, align_dir=align_dir,
+                reads_dir=reads_dir, raw_reads_dir=raw_reads_dir)
             if not header_written:
                 outf.write('\t'.join(map(str, header))+'\n')
                 header_written = True
@@ -100,6 +117,10 @@ def parser_assembly_stats(parser=argparse.ArgumentParser()):
         help='Directory with assembly temp files. (default: %(default)s)')
     parser.add_argument('--align_dir',     default='data/02_align_to_self',
         help='Directory with reads aligned to own assembly. (default: %(default)s)')
+    parser.add_argument('--reads_dir',     default='data/01_per_sample',
+        help='Directory with unaligned filtered read BAMs. (default: %(default)s)')
+    parser.add_argument('--raw_reads_dir', default='data/00_raw',
+        help='Directory with unaligned raw read BAMs. (default: %(default)s)')
     util.cmd.attach_main(parser, assembly_stats, split_args=True)
     return parser
 __commands__.append(('assembly_stats', parser_assembly_stats))
@@ -110,31 +131,6 @@ def get_refalign_stats(sample):
     pass
 
 
-def consolidate_bamstats(inFiles, outFile):
-    '''Consolidate multiple bamstats reports into one.'''
-    with util.file.open_or_gzopen(outFile, 'wt') as outf:
-        header = []
-        out_n = 0
-        for fn in inFiles:
-            out = {}
-            with util.file.open_or_gzopen(fn, 'rt') as inf:
-                for line in inf:
-                    k,v = line.rstrip('\n').split('\t')
-                    out[k] = v
-                    if out_n==0:
-                        header.append(k)
-            if out_n==0:
-                outf.write('\t'.join(header)+'\n')
-            outf.write('\t'.join([out.get(h,'') for h in header])+'\n')
-            out_n += 1
-def parser_consolidate_bamstats(parser=argparse.ArgumentParser()):
-    parser.add_argument('inFiles', help='Input report files.', nargs='+')
-    parser.add_argument('outFile', help='Output report file.')
-    util.cmd.attach_main(parser, consolidate_bamstats, split_args=True)
-    return parser
-__commands__.append(('consolidate_bamstats', parser_consolidate_bamstats))
-
-
 
 def consolidate_fastqc(inDirs, outFile):
     '''Consolidate multiple FASTQC reports into one.'''
@@ -200,80 +196,14 @@ def get_earliest_date(inDir):
     earliest = min(os.path.getmtime(fn) for fn in fnames)
     return time.strftime("%Y-%m-%d", time.localtime(earliest))
 
-def coverage_summary(inFiles, ending, outFile, runFile=None, statsDir=None, thresholds=(1,5,20,100)):
-    seqinfo = runFile and get_lib_info(runFile) or {}
-    baminfo = statsDir and get_bam_info(statsDir) or {}
-    with util.file.open_or_gzopen(outFile, 'wt') as outf:
-        header = ['library'] + ['sites_cov_%dX'%t for t in thresholds] + ['median_cov', 'mean_cov', 'mean_non0_cov']
-        header_bam = ['reads_total', 'reads_non_Hs_rmdup', 'reads_EBOV', 'reads_EBOV_rmdup']
-        header_seq = ['sample','seq_flowcell_lane', 'seq_mux_barcode', 'seq_plate_well', 'seq_date', 'KGH_Tube_ID']
-        if baminfo:
-            header += header_bam
-        if seqinfo:
-            header += header_seq
-        outf.write('\t'.join(header)+'\n')
-        for fn in inFiles:
-            if not fn.endswith(ending):
-                raise Exception()
-            s = os.path.basename(fn)[:-len(ending)]
-            with util.file.open_or_gzopen(fn, 'rt') as inf:
-                coverages = list(int(line.rstrip('\n').split('\t')[2]) for line in inf)
-            out = [sum(1 for n in coverages if n>=thresh) for thresh in thresholds]
-            out = [s] + out
-            out +=[median(coverages), "%0.3f"%mean(coverages),
-                "%0.3f"%mean([n for n in coverages if n>0])]
-            if baminfo:
-                if s in baminfo:
-                    out += [baminfo[s].get(adj,'') for adj in ('raw', 'cleaned', 'ref_mapped', 'ref_rmdup')]
-                else:
-                    out += ['' for h in header_bam]
-            if seqinfo:
-                if s in seqinfo:
-                    out += [','.join(util.misc.unique(run[i] for run in seqinfo[s]))
-                        for i in range(len(header_seq))]
-                else:
-                    out += ['' for h in header_seq]
-            outf.write('\t'.join(map(str,out))+'\n')
-def parser_coverage_summary(parser=argparse.ArgumentParser()):
-    parser.add_argument('coverageDir', help='Input coverage report directory.')
-    parser.add_argument('coverageSuffix', help='Suffix of all coverage files.')
-    parser.add_argument('outFile', help='Output report file.')
-    parser.add_argument('--runFile', help='Link in plate info from seq runs.', default=None)
-    parser.add_argument('--bamstatsDir', help='Link in read info from BAM alignments.', default=None)
-    util.cmd.attach_main(parser, main_coverage_summary)
-    return parser
-def main_coverage_summary(args):
-    '''Produce summary stats of genome coverage.'''
-    inFiles = list(glob.glob(os.path.join(args.coverageDir, "*"+args.coverageSuffix)))
-    coverage_summary(inFiles, args.coverageSuffix, args.outFile, args.runFile, args.bamstatsDir)
-    return 0
-__commands__.append(('coverage_summary', parser_coverage_summary))
-
-def consolidate_coverage(inFiles, adj, outFile):
-    '''Consolidate multiple coverage reports into one.'''
-    ending = '.coverage_%s.txt' % adj
-    with util.file.open_or_gzopen(outFile, 'wt') as outf:
-        for fn in inFiles:
-            if not fn.endswith(ending):
-                raise Exception()
-            s = os.path.basename(fn)[:-len(ending)]
-            with open(fn, 'rt') as inf:
-                for line in inf:
-                    outf.write(line.rstrip('\n') + '\t' + s + '\n')
-def parser_consolidate_coverage(parser=argparse.ArgumentParser()):
-    parser.add_argument('inFiles', help='Input coverage files.', nargs='+')
-    parser.add_argument('adj', help='Report adjective.')
-    parser.add_argument('outFile', help='Output report file.')
-    util.cmd.attach_main(parser, consolidate_coverage, split_args=True)
-    return parser
-__commands__.append(('consolidate_coverage', parser_consolidate_coverage))
 
 
 
-def consolidate_spike_count(inFiles, outFile):
+def consolidate_spike_count(inDir, outFile):
     '''Consolidate multiple spike count reports into one.'''
     with open(outFile, 'wt') as outf:
-        for fn in inFiles:
+        for fn in os.listdir(inDir):
+            fn = os.path.join(inDir, fn)
             s = os.path.basename(fn)
             if not s.endswith('.spike_count.txt'):
                 raise Exception()
@@ -284,7 +214,7 @@ def consolidate_spike_count(inFiles, outFile):
                         spike, count = line.strip().split('\t')
                         outf.write('\t'.join([s, spike, count])+'\n')
 def parser_consolidate_spike_count(parser=argparse.ArgumentParser()):
-    parser.add_argument('inFiles', help='Input coverage files.', nargs='+')
+    parser.add_argument('inDir', help='Input spike count directory.')
     parser.add_argument('outFile', help='Output report file.')
     util.cmd.attach_main(parser, consolidate_spike_count, split_args=True)
     return parser
diff --git a/tools/trinity.py b/tools/trinity.py
index 249779157..8df9bee01 100644
--- a/tools/trinity.py
+++ b/tools/trinity.py
@@ -18,6 +18,7 @@
 
 
 class TrinityTool(tools.Tool) :
+    jvmMemDefault = '4g'
     def __init__(self, install_methods = None) :
         if install_methods == None :
             install_methods = [
@@ -28,10 +29,14 @@ def __init__(self, install_methods = None) :
     def version(self) :
         return tool_version
     
-    def execute(self, inFastq1, inFastq2, outFasta, min_contig_length=300):
+    def execute(self, inFastq1, inFastq2, outFasta, min_contig_length=300,
+            JVMmemory=None):
+        if JVMmemory==None:
+            JVMmemory = self.jvmMemDefault
         outdir = tempfile.mkdtemp(prefix='trinity-')
         cmd = [self.install_and_get_path(),
-            '--CPU', '1',
+            '--CPU', '2',
+            '--bflyHeapSpace', JVMmemory.upper(),
             '--min_contig_length', str(min_contig_length),
             '--seqType', 'fq',
             '--left', inFastq1,