diff --git a/src/map/include/computeMap.hpp b/src/map/include/computeMap.hpp
index e91fc447..47ac8b64 100644
--- a/src/map/include/computeMap.hpp
+++ b/src/map/include/computeMap.hpp
@@ -152,7 +152,7 @@ namespace skch
                     if (param.filterMode == filter::ONETOONE)
                         qmetadata.push_back( ContigInfo{seq_name, len} );
                     //Is the read too short?
-                    if(len < param.windowSize || len < param.kmerSize || len < param.segLength)
+                    if(len < param.windowSize || len < param.kmerSize)
                     {
 //#ifdef DEBUG
                         std::cerr << "WARNING, skch::Map::mapQuery, read is not long enough for mapping" << std::endl;
@@ -215,7 +215,7 @@ namespace skch
         //save query sequence name
         output->qseqName = input->seqName;
 
-        if(! param.split)   
+        if(! param.split || input->len <= param.segLength)
         {
           QueryMetaData <MinVec_Type> Q;
           Q.seq = &(input->seq)[0u];
@@ -294,7 +294,10 @@ namespace skch
         //filter mappings best over query sequence axis
         if(param.filterMode == filter::MAP || param.filterMode == filter::ONETOONE)
         {
-            skch::Filter::query::filterMappings(output->readMappings, param.secondaryToKeep);
+            skch::Filter::query::filterMappings(output->readMappings,
+                                                (input->len < param.segLength ?
+                                                 param.shortSecondaryToKeep
+                                                 : param.secondaryToKeep));
         }
 
         //Make sure mapping boundary don't exceed sequence lengths
diff --git a/src/map/include/map_parameters.hpp b/src/map/include/map_parameters.hpp
index 034cc5b7..51b5c7b0 100644
--- a/src/map/include/map_parameters.hpp
+++ b/src/map/include/map_parameters.hpp
@@ -26,6 +26,7 @@ struct Parameters
     float percentageIdentity;                         //user defined threshold for good similarity
     int filterMode;                                   //filtering mode in mashmap
     int secondaryToKeep;                              //how many secondary alignments we keep
+    int shortSecondaryToKeep;                         //how many secondary alignments we keep for reads < segLength
     int threads;                                      //execution thread count
     std::vector<std::string> refSequences;            //reference sequence(s)
     std::vector<std::string> querySequences;          //query sequence(s)
diff --git a/src/yeet/include/parse_args.hpp b/src/yeet/include/parse_args.hpp
index 5d695f85..540dbf99 100644
--- a/src/yeet/include/parse_args.hpp
+++ b/src/yeet/include/parse_args.hpp
@@ -40,6 +40,7 @@ void parse_args(int argc,
     args::ValueFlag<int> kmer_size(parser, "N", "kmer size <= 16 [default: 16]", {'k', "kmer"});
     args::ValueFlag<std::string> map_filter_mode(parser, "MODE", "filter mode for map step, either 'map', 'one-to-one', or 'none' [default: map]", {'f', "map-filter-mode"});
     args::ValueFlag<int> map_secondaries(parser, "N", "number of secondary mappings to retain in 'map' filter mode (total number of mappings is this + 1) [default: 0]", {'n', "n-secondary"});
+    args::ValueFlag<int> map_short_secondaries(parser, "N", "number of secondary mappings to retain for sequences shorter than segment length [default: 0]", {'S', "n-short-secondary"});
     args::Flag skip_self(parser, "", "skip self mappings when the query and target name is the same (for all-vs-all mode)", {'X', "skip-self"});
     args::ValueFlag<char> skip_prefix(parser, "C", "skip mappings when the query and target have the same prefix before the given character C", {'Y', "skip-prefix"});
     args::Flag approx_mapping(parser, "approx-map", "skip base-level alignment, producing an approximate mapping in PAF", {'m',"approx-map"});
@@ -218,6 +219,12 @@ void parse_args(int argc,
         map_parameters.secondaryToKeep = 0;
     }
 
+    if (map_short_secondaries) {
+        map_parameters.shortSecondaryToKeep = args::get(map_short_secondaries);
+    } else {
+        map_parameters.shortSecondaryToKeep = 0;
+    }
+
     if (skip_self) {
         map_parameters.skip_self = true;
     } else {