lh3/seqtk issues and pull requests

#216 - zip, outfile

Issue - State: closed - Opened by emgiles about 1 month ago - 1 comment

#215 - seqtk telo can't find results with my data

Issue - State: open - Opened by ksc289 3 months ago - 6 comments

#214 - Error

Issue - State: open - Opened by aupadrasta 4 months ago - 1 comment

#213 - `sample` command silently produces incorrect empty reads

Issue - State: open - Opened by rickymagner 5 months ago - 1 comment

#212 - subseq silent fail on malformatted fq

Issue - State: open - Opened by cmsoulette 5 months ago

#211 - CutN fails when sequence begins with Ns

Issue - State: open - Opened by hloucks 5 months ago

#210 - Quality scores

Issue - State: closed - Opened by lskatz 6 months ago - 1 comment

#209 - converting fasta to fastq

Issue - State: open - Opened by keecarter 6 months ago - 2 comments

#208 - buggy behavior with seqtk subseq command

Issue - State: closed - Opened by franciscozorrilla 7 months ago - 1 comment

#207 - DNS Resolution Warning with Singularity Container

Issue - State: open - Opened by ua-micro-cha 8 months ago

#206 - Is the "sample" feature subsampling without replacement?

Issue - State: closed - Opened by AprilJauhal 8 months ago - 1 comment

#205 - `seqtk hpc input.fq` ignores the quality and converts to .fa

Issue - State: open - Opened by aafshinfard 9 months ago

#204 - seqtk_telomere_reads_output

Pull Request - State: open - Opened by Wenfei-Xian 11 months ago

#203 - Seqtk to count sequences same SeqID

Issue - State: closed - Opened by silvia1234567890 about 1 year ago

#202 - seqtk comp count CpG

Issue - State: open - Opened by linpei26 about 1 year ago

#201 - seqtk telo -m works partially with 8mer wasp telomere

Issue - State: open - Opened by jbh-cas over 1 year ago - 5 comments

#200 - output file contains only one amino acid

Issue - State: open - Opened by Jiayi-Zheng over 1 year ago - 1 comment

#199 - Problem with seqtk sample

Issue - State: closed - Opened by SplitInf almost 2 years ago - 1 comment

#198 - seqtk produces different number of reads for paired end files

Issue - State: closed - Opened by ruy-jauregui almost 2 years ago - 1 comment
Labels: question

#197 - Question: DNA string compressing

Issue - State: closed - Opened by jianshu93 about 2 years ago - 1 comment

#196 - The output file size of seqtk subseq is zero

Issue - State: closed - Opened by CherryX727 about 2 years ago - 1 comment
Labels: question

#195 - ERROR: the 2nd file has fewer records

Issue - State: closed - Opened by mbk0asis over 2 years ago - 1 comment

#194 - seqtk sample can't properly output fastq.gz

Issue - State: closed - Opened by soappp9527 over 2 years ago - 1 comment

#193 - seqtk sample not working as expected

Issue - State: closed - Opened by antoine4ucsd over 2 years ago - 2 comments

#192 - support >2G sequences

Pull Request - State: closed - Opened by c-zhou over 2 years ago - 1 comment

#191 - `seqtk seq` segfaults on 10G scaffolds

Issue - State: closed - Opened by mcshane over 2 years ago - 4 comments

#190 - seqtk sample: with out without replacement?

Issue - State: closed - Opened by erajshafiq over 2 years ago - 1 comment

#189 - subseq empty output

Issue - State: open - Opened by SingleCellCRM-user over 2 years ago

#188 - feature request: ability to pass through all reads by specifying sample '1.0'

Issue - State: open - Opened by eboyden over 2 years ago

#187 - cutN penalty to identify all Ns?

Issue - State: open - Opened by nikostr over 2 years ago

#186 - Fail to open input file/stream

Issue - State: open - Opened by XueWang2019 almost 3 years ago - 1 comment

#185 - seqtk hrun bin size

Issue - State: open - Opened by kimin0402 almost 3 years ago - 1 comment

#184 - Seqtk trimfq used on files in .gz format returns much larger files but still .gz

Issue - State: closed - Opened by bmillerlab almost 3 years ago - 1 comment

#183 - Merging multiple fastq.gz files

Issue - State: closed - Opened by baigal628 almost 3 years ago - 2 comments

#182 - Add LDFLAGS CPPFLAGS and unshadow CFLAGS

Pull Request - State: open - Opened by mr-c almost 3 years ago

#181 - seq comp documentation per #47

Pull Request - State: open - Opened by lskatz almost 3 years ago - 1 comment

#180 - seqtk subseq in.fq name.lst > out.fq didn't work

Issue - State: closed - Opened by li0604 about 3 years ago - 4 comments

#179 - make warning

Issue - State: closed - Opened by chenling-immunai about 3 years ago - 4 comments

#178 - Seqkit

Issue - State: closed - Opened by Agat007-34 about 3 years ago - 1 comment

#177 - error running seqtk with parallel

Issue - State: open - Opened by EduanWilkinson about 3 years ago - 1 comment

#176 - Error: Unable to locate package seqtk

Issue - State: open - Opened by HanaBanan over 3 years ago - 1 comment

#175 - Packaging

Issue - State: open - Opened by V-Z over 3 years ago

#174 - Extract sequences in regions doesn't work?

Issue - State: open - Opened by deb0612 over 3 years ago

#173 - output as compressed?

Issue - State: closed - Opened by ahdee over 3 years ago - 2 comments

#172 - Hi

Issue - State: open - Opened by kaurravneet4123 over 3 years ago - 2 comments

#171 - Problems with seqtk rename on fastq files with long reads (like isoseq)

Issue - State: open - Opened by maol-corteva over 3 years ago - 1 comment

#170 - Not sorting /1 and /2 reads properly.

Issue - State: closed - Opened by jallmer over 3 years ago - 1 comment

#169 - Subseq extracting reads with query name list failed

Issue - State: open - Opened by yangyxt over 3 years ago - 1 comment

#168 - Add prefixsplit function

Pull Request - State: open - Opened by Tixii over 3 years ago

#167 - fastq record in wrong order

Issue - State: closed - Opened by sunfenghao2017 over 3 years ago - 1 comment

#166 - Problems during installation

Issue - State: closed - Opened by naurasd over 3 years ago - 2 comments

#165 - README.md points to package in common Linux distros

Pull Request - State: open - Opened by smoe almost 4 years ago

#164 - Sample ignores reads zero length reads

Issue - State: open - Opened by nh13 almost 4 years ago

#163 - problem installing/running

Issue - State: open - Opened by ctob2 almost 4 years ago - 1 comment

#162 - subsample reads from an interleaved fastq file

Issue - State: closed - Opened by fgvieira about 4 years ago - 1 comment

#161 - could not ‘make’ in gcc 10.1.0 manjaro

Issue - State: closed - Opened by shinepreventer about 4 years ago - 1 comment

#160 - Have cutN report N:s also at beginning of sequence

Pull Request - State: open - Opened by kpalin over 4 years ago

#159 - [feature] kmer counting

Issue - State: closed - Opened by shouldsee over 4 years ago - 3 comments

#158 - Seqtk sample ignores random seed

Issue - State: closed - Opened by MatthewRalston over 4 years ago - 1 comment

#157 - Subseq exclude list

Issue - State: open - Opened by OnlyHigh over 4 years ago - 1 comment

#156 - Retrieve paired-end reads with their mates

Issue - State: open - Opened by iquasere over 4 years ago - 1 comment

#155 - sampling compressed files

Issue - State: closed - Opened by dalilasss over 4 years ago - 6 comments

#154 - set seed with different samples

Issue - State: closed - Opened by kaiwang12 over 4 years ago - 1 comment
Labels: question

#153 - Add help to the cli and README for split

Pull Request - State: closed - Opened by ljyanesm over 4 years ago - 1 comment

#152 - Extract Sequences in a Defined Order

Issue - State: open - Opened by perryguog almost 5 years ago

#151 - Can seqtk extract first xx nt from the left end or right end

Issue - State: closed - Opened by Edison2021 almost 5 years ago

#150 - the size of file is different

Issue - State: closed - Opened by Hulanyue almost 5 years ago - 1 comment

#149 - fastqc outofmemoryError from seqtk generated files

Issue - State: open - Opened by wbsimey almost 5 years ago - 1 comment

#148 - Add '-E max_len' to 'seqtk seq'

Pull Request - State: open - Opened by tseemann almost 5 years ago

#147 - add argument -o to seqtk sample to output sampled library to zip file

Pull Request - State: closed - Opened by wulj2 about 5 years ago

#146 - Unusual behavior due to asterix shell expansion

Issue - State: closed - Opened by deprekate about 5 years ago - 2 comments

#145 - seqtk sample gives empty output

Issue - State: closed - Opened by Gil-marquez about 5 years ago - 3 comments

#144 - f

Issue - State: closed - Opened by Gil-marquez about 5 years ago

#143 - seqtk subseq inserting line break after 1024 characters

Issue - State: closed - Opened by nqp3 about 5 years ago - 4 comments

#142 - Update Makefile to play nice with bioconda

Pull Request - State: closed - Opened by andersgs about 5 years ago

#141 - seqtk subseq error id with whitespace

Issue - State: closed - Opened by fengyq about 5 years ago - 2 comments

#140 - Could not allocate enough memory for 90576558080 sequences

Issue - State: open - Opened by Antony-1996 about 5 years ago - 2 comments

#139 - Failure to covert Fastq to fastA

Issue - State: closed - Opened by orchid677 over 5 years ago - 2 comments

#138 - modified a typo in the license

Pull Request - State: open - Opened by lidd77 over 5 years ago

#137 - what does the meanning of '-Wno-unused-function' ?

Issue - State: closed - Opened by lidd77 over 5 years ago - 3 comments

#136 - Can seqtk filter the reads by length?

Issue - State: open - Opened by henganl2 over 5 years ago - 1 comment

#135 - Sample Command Doesn't Work With Process Substitution

Issue - State: closed - Opened by DarioS over 5 years ago - 1 comment

#134 - Request: Add seqtk shuffle command to randomise order of reads

Issue - State: open - Opened by peterjc over 5 years ago - 1 comment

#133 - add -r for stk_subseq to remove seq

Pull Request - State: open - Opened by alienzj over 5 years ago - 2 comments

#132 - add -r for stk_subseq to remove seq

Pull Request - State: closed - Opened by alienzj over 5 years ago - 1 comment

#131 - Type conversion from void* to unsigned char*

Pull Request - State: closed - Opened by cjain7 over 5 years ago - 1 comment

#130 - Add some structure to the code

Issue - State: closed - Opened by kounkou over 5 years ago

#129 - Adding some structure to the code

Pull Request - State: closed - Opened by kounkou over 5 years ago - 2 comments

#128 - subseq -t

Issue - State: closed - Opened by MrLocuace over 5 years ago - 3 comments

#127 - install error

Issue - State: closed - Opened by xiaohongniua almost 6 years ago - 1 comment

#126 - compiling error

Issue - State: closed - Opened by ldutoit almost 6 years ago - 2 comments

#125 - Cleanup Makefile to respect users environment.

Pull Request - State: open - Opened by mmokrejs almost 6 years ago - 1 comment

#124 - seq -A identifies ">" in FASTQ as FASTA header

Issue - State: closed - Opened by ZeweiSong almost 6 years ago - 4 comments

#123 - improve parsing performance

Pull Request - State: closed - Opened by kloetzl almost 6 years ago - 1 comment

GitHub / lh3/seqtk issues and pull requests