Check and ignore unmapped reads Updated default consensus to -m 1- -n N Check BED file format GFF3 lines with # ignored Handle overlapping primers by taking minimum of start pos of primers for forward reads and maximum of end position of primers for reverse reads
RaxML exclude file for 13 plastome, 145,064 base pair alignment; 1075 segments excluded based on GBL...
28S ribosomal DNA nexus file. Aligned with MAFFT, ambiguously aligned regions removed using GBLOCKS ...
S12A Text. Reasoner input constraints for the 2015./2014.Pelecanimorphae alignment, with coverage lo...
Fixed bug (#36) if deletion at final position of primer region. BED file (-b) now optional for ivar ...
iVar v1.0 has the following functions. Trimming primer sequences and low quality Call variants Filt...
Fixes #42 specifically for unpaired reads that span only 1 primer. Removes uninitialized errors wit...
New parameter added to consensus calling to allow insertions to be called at a different threshold t...
ivar trim now has -k flag to mark all reads that fail filters as BAM_FQCFAIL and write to output BAM...
Removed excess insertionSort calls in PR #155 to address speed issues in ivar trim from issue #154 ...
Discarded quality checks for INDELS. Added -e flag to allow reads without primers to go through
ivar trim now has -x flag to specify an offset to search for primer positions. This allows for trimm...
What's Changed Fixed issues with streaming/piping for ivar trim functionality by addressing a bug i...
New flag QC FAIL to ivar trim -i option to name FASTA header in ivar consensus Bug fixes for memory ...
Rapid multiple sequence alignment and consensus sequence generation using MUSCLE
Commits 1204f61: Better make these noinline to avoid churn. (Troels Henriksen) 57fc1d5: Avoid zero-...
RaxML exclude file for 13 plastome, 145,064 base pair alignment; 1075 segments excluded based on GBL...
28S ribosomal DNA nexus file. Aligned with MAFFT, ambiguously aligned regions removed using GBLOCKS ...
S12A Text. Reasoner input constraints for the 2015./2014.Pelecanimorphae alignment, with coverage lo...
Fixed bug (#36) if deletion at final position of primer region. BED file (-b) now optional for ivar ...
iVar v1.0 has the following functions. Trimming primer sequences and low quality Call variants Filt...
Fixes #42 specifically for unpaired reads that span only 1 primer. Removes uninitialized errors wit...
New parameter added to consensus calling to allow insertions to be called at a different threshold t...
ivar trim now has -k flag to mark all reads that fail filters as BAM_FQCFAIL and write to output BAM...
Removed excess insertionSort calls in PR #155 to address speed issues in ivar trim from issue #154 ...
Discarded quality checks for INDELS. Added -e flag to allow reads without primers to go through
ivar trim now has -x flag to specify an offset to search for primer positions. This allows for trimm...
What's Changed Fixed issues with streaming/piping for ivar trim functionality by addressing a bug i...
New flag QC FAIL to ivar trim -i option to name FASTA header in ivar consensus Bug fixes for memory ...
Rapid multiple sequence alignment and consensus sequence generation using MUSCLE
Commits 1204f61: Better make these noinline to avoid churn. (Troels Henriksen) 57fc1d5: Avoid zero-...
RaxML exclude file for 13 plastome, 145,064 base pair alignment; 1075 segments excluded based on GBL...
28S ribosomal DNA nexus file. Aligned with MAFFT, ambiguously aligned regions removed using GBLOCKS ...
S12A Text. Reasoner input constraints for the 2015./2014.Pelecanimorphae alignment, with coverage lo...
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