shenwei356/seqkit: SeqKit v2.0.0

Changelogs SeqKit v2.0.0 - 2021-08-27 Performance improvements seqkit: faster FASTA/Q reading and writing, especially on FASTQ, see the benchmark. reading (plain text): 4X faster. seqkit stats dataset_C.fq reading (gzip files): 45% faster. seqkit stats dataset_C.fq.gz reading + writing (plain text): 3.5X faster. seqkit grep -p . -v dataset_C.fq -o t reading + writing (gzip files): 2.2X faster. seqkit grep -p . -v dataset_C.fq.gz -o t.gz change default value of -j/--threads from 2 to 4, which is faster for writting gzip files. seqkit seq: fix writing speed, which was slowed down in v0.12.1. Breaking changes seqkit grep/rmdup/common: consider reverse complement sequence by default for comparing by sequence, add flag -P/--only-positive-strand. #215 seqkit rename: rename ID only, do not append original header to new ID. #236 seqkit fx2tab: for -s/--seq-hash: outputing MD5 instead of hash value (integers) of xxhash. #219 Bugfixes seqkit seq: fix failing to output gzipped format for file name with extension of .gz since v0.12.1. seqkit tab2fx: fix bug for very long sequences. #214 seqkit fish: fix range check. #213 seqkit grep: it's not exactly a bug: forgot to use multi-threads for -m > 0. New features/enhancements seqkit grep: allow empty pattern files. seqkit faidx: support region with begin > end, i.e., returning reverse complement sequence add new flag -l/--region-file: file containing a list of regions. seqkit fx2tab: new flag -Q/--no-qual for disabling outputing quality even for FASTQ file. #221 seqkit amplicon: new flag -u/--save-unmatched for saving records that do not match any primer. seqkit sort: new flag -b/--by-bases for sorting by non-gap bases, for multiple sequence alignment files.#216 Download SeqKit is implemented in Go programming language, statically-linked executable binary files are freely available. Please cite: W Shen, S Le, Y Li*, F Hu*. SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation. PLOS ONE. doi:10.1371/journal.pone.0163962. OS Arch File, 中国镜像 Download Count Linux 32-bit seqkit_linux_386.tar.gz, 中国镜像 Linux 64-bit seqkit_linux_amd64.tar.gz, 中国镜像 Linux arm64 seqkit_linux_arm64.tar.gz, 中国镜像 macOS 64-bit seqkit_darwin_amd64.tar.gz, 中国镜像 macOS arm64 seqkit_darwin_arm64.tar.gz, 中国镜像 Windows 32-bit seqkit_windows_386.exe.tar.gz, 中国镜像 Windows 64-bit seqkit_windows_amd64.exe.tar.gz, 中国镜像 Notes please open an issuse to request binaries for other platforms. run seqkit version to check update !!! run seqkit genautocomplete to update shell autocompletion script !!