Changes from v0.46.0<\/p>\n\n
Adds the inDrops technologies (versions 2 and 3)<\/p>\n\n
This version adds the option running the Changes from v0.45.0<\/p>\n\n This version adds the option of specifying an arbitrary single cell technology for the Bug fixes<\/p>\n\n Issue 201: Pseudobam was not being run unless bootstrap was also performed\nIssue 199: Error when reading UMI files for the pseudo mode.<\/p>\n\n Changes from v0.44.0<\/p>\n\n To process single cell data run Changes from v0.43.1<\/p>\n\n Adds a Adds QC information to The added fields are<\/p>\n Changes from v0.43.0<\/p>\n\n kallisto can now find reads which span potential fusion breakpoints. The Switched to a uniform point for the EM algorithm that works better in highly ambiguous cases.<\/p>\n\n Several fixes to the pseudobam output so that the resulting SAM\/BAM file can be validated with picard.<\/p>\n\n Changes from v0.42.5<\/p>\n\n Quantification can now be run in strand specific mode. The experiment can either be Changes from v0.42.4<\/p>\n\n A new mode kallisto pseudo has been implemented which allows reads to only be pseudoaligned.\nThis mode is useful during single cell analysis as many different experiments (single cells)\ncan be analyzed at the same time and their equivalence classes will be consistent.\nIt will also output a matrix of equivalence class counts (as used in\nFast and accurate single-cell RNA-Seq analysis by clustering of transcript-compatibility counts<\/a>).<\/p>\n\n Kallisto has been published in Nature Biotechnology (2016)<\/p>\n\n Bray, N. L., Pimentel, H., Melsted, P. & Pachter, L. Near-optimal probabilistic RNA-seq quantification. Nat Biotech<\/em> 34, 525\u2013527 (2016).\ndoi:10.1038\/nbt.3519<\/a><\/p>\n<\/blockquote>\n\n","link":"https:\/\/pachterlab.github.io\/kallisto\/releases\/2016\/04\/04\/v0.42.5","guid":"https:\/\/pachterlab.github.io\/kallisto\/releases\/2016\/04\/04\/v0.42.5","pubDate":"2016-04-04T00:00:00+00:00"},{"title":"V0.42.4","description":" Changes from v0.42.3<\/p>\n\n It is recommended that users upgrade to this release for maximum performance.<\/p>\n","link":"https:\/\/pachterlab.github.io\/kallisto\/releases\/2015\/10\/29\/v0.42.4","guid":"https:\/\/pachterlab.github.io\/kallisto\/releases\/2015\/10\/29\/v0.42.4","pubDate":"2015-10-29T00:00:00+00:00"},{"title":"V0.42.3","description":" Changes from v0.42.2.1<\/p>\n\n It is recommended that users upgrade to this release for compatibility with sleuth<\/a><\/p>\n\n","link":"https:\/\/pachterlab.github.io\/kallisto\/releases\/2015\/08\/25\/v0.42.3","guid":"https:\/\/pachterlab.github.io\/kallisto\/releases\/2015\/08\/25\/v0.42.3","pubDate":"2015-08-25T00:00:00+00:00"},{"title":"V0.42.2.1","description":" A few bugfixes to v0.42.2 are included here:<\/p>\n\n It is recommended that users upgrade to this release.<\/p>\n\n","link":"https:\/\/pachterlab.github.io\/kallisto\/releases\/2015\/07\/06\/v0.42.2.1","guid":"https:\/\/pachterlab.github.io\/kallisto\/releases\/2015\/07\/06\/v0.42.2.1","pubDate":"2015-07-06T00:00:00+00:00"},{"title":"V0.42.2","description":" This is version 0.42.2 of Kallisto.<\/p>\n\n Updates include<\/p>\n\n This is version 0.42.1 of Kallisto. We recommend that users upgrade to this version.<\/p>\n\n Updates include<\/p>\n\n This is the initial public release of Kallisto.<\/p>\n\n","link":"https:\/\/pachterlab.github.io\/kallisto\/releases\/2015\/05\/06\/v0.42","guid":"https:\/\/pachterlab.github.io\/kallisto\/releases\/2015\/05\/06\/v0.42","pubDate":"2015-05-06T00:00:00+00:00"}]}}bus<\/code> command on processed BAM files.<\/p>\n","link":"https:\/\/pachterlab.github.io\/kallisto\/releases\/2019\/10\/04\/v0.46.1","guid":"https:\/\/pachterlab.github.io\/kallisto\/releases\/2019\/10\/04\/v0.46.1","pubDate":"2019-10-04T00:00:00+00:00"},{"title":"V0.46.0","description":"BUS<\/h1>\n
bus<\/code> command in kallisto.\nAlso 10xv3 as a technology option for the bus command.<\/p>\n\n-l<\/code> flag for bus was inactive.<\/p>\n","link":"https:\/\/pachterlab.github.io\/kallisto\/releases\/2019\/06\/12\/v0.46.0","guid":"https:\/\/pachterlab.github.io\/kallisto\/releases\/2019\/06\/12\/v0.46.0","pubDate":"2019-06-12T00:00:00+00:00"},{"title":"V0.45.0","description":"BUS<\/h1>\n\n
kallisto<\/code> can now process raw FASTQ files for single cell RNA-Seq and create an output in BUS format<\/a> which can be further processed using bustools<\/a><\/p>\n\nkallisto<\/code> with the bus<\/code> command. To see a list of supported technologies, run with the --list<\/code> option<\/p>\n\n> kallisto bus --list \nList of supported single cell technologies\n\nshort name description\n---------- -----------\n10Xv1 10X chemistry version 1\n10Xv2 10X chemistry verison 2\nDropSeq DropSeq\ninDrop inDrop\nCELSeq CEL-Seq\nCELSeq2 CEL-Seq version 2\nSCRBSeq SCRB-Seq\n<\/code><\/pre><\/div><\/div>\n\n","link":"https:\/\/pachterlab.github.io\/kallisto\/releases\/2018\/11\/17\/v0.45.0","guid":"https:\/\/pachterlab.github.io\/kallisto\/releases\/2018\/11\/17\/v0.45.0","pubDate":"2018-11-17T00:00:00+00:00"},{"title":"V0.44.0","description":"BAM!<\/h1>\n\n
kallisto<\/code> can now project pseudoalignments from transcripts down to genomic coordinates. This requires a GTF file corresponding to the transcriptome used to construct the index. The resulting BAM file is sorted by genomic coordinates and indexed.<\/p>\n\n\n
--pseudobam<\/code> option works as before in transcript coordinates, but creates a single output pseudoalignments.bam<\/code> in the output folder. This mode no longer writes SAM format to standard output, but writes the binary BAM file directly. Multithreaded --pseudobam<\/code> works now<\/li>\n --genomebam<\/code> option writes pseudoalignments to the file pseudoalignments.bam<\/code> in sorted genomic coordinates, requires a --gtf<\/code> option and optionally a --chromosomes<\/code> options set.<\/li>\n<\/ul>\n\nquant mode<\/h3>\n\n
--single-overhang<\/code> option that does not discard reads where unobserved rest of fragment is predicted to lie outside a transcript. This is mainly useful for mapping 3\u2019 biased reads from single cell experiments.<\/p>\n\nJSON output<\/h3>\n\n
run_info.json<\/code> in the output folder<\/p>\n\n\n
n_pseudoaligned<\/code> : number of fragments that could be pseudoaligned<\/li>\n p_pseudoaligned<\/code> : percentage of fragments that could be pseudoaligned<\/li>\n n_unique<\/code> : number of fragments that could be pseudoaligned to a unique target sequence<\/li>\n p_unique<\/code> : percentage of fragments that could be pseudoaligned to a unique target sequence<\/li>\n<\/ul>\n","link":"https:\/\/pachterlab.github.io\/kallisto\/releases\/2018\/01\/29\/v0.44.0","guid":"https:\/\/pachterlab.github.io\/kallisto\/releases\/2018\/01\/29\/v0.44.0","pubDate":"2018-01-29T00:00:00+00:00"},{"title":"V0.43.1","description":"fusions<\/h3>\n\n
quant<\/code> mode adds a --fusion<\/code> flag which identifies read pairs involved in fusions and writes output to fusion.txt<\/code>, this file is then processed by pizzly<\/code> for downstream analysis.<\/p>\n\nquant mode:<\/h3>\n\n
pseudobam fixes<\/h3>\n\n
Bug fixes<\/h3>\n\n
\n
nan<\/code> for tpm values)<\/li>\n<\/ul>\n","link":"https:\/\/pachterlab.github.io\/kallisto\/releases\/2017\/03\/20\/v0.43.1","guid":"https:\/\/pachterlab.github.io\/kallisto\/releases\/2017\/03\/20\/v0.43.1","pubDate":"2017-03-20T00:00:00+00:00"},{"title":"V0.43.0","description":"quant mode:<\/h3>\n\n
--fr-stranded<\/code>, when the first read is on the forward strand or --rf-stranded<\/code> when the first read is on the second strand.<\/p>\n\npseudo mode:<\/h3>\n\n
\n
pseudo mode:<\/h3>\n\n
Bug fixes:<\/h3>\n\n
\n
Citation<\/h3>\n\n
\n
\n
\n
'aux\/num_processed'<\/code> to H5<\/li>\n 'inspect'<\/code><\/li>\n \n
-nan<\/code> values would sometimes show up in abundances in edge case<\/li>\n<\/ul>\n\n\n
index<\/code>\n \n
quant<\/code>\n \n
-t<\/code> to specify number of threads<\/li>\n kallisto<\/code> will check the transcript positions to discard reads that would go outside of transcript given the mean fragment length.<\/li>\n kallisto<\/code> can learn a model for sequence specific bias and correct the abundances accordingly.<\/li>\n .tsv<\/code> ending.<\/li>\n <\/ul>\n <\/li>\n<\/ul>\n\n","link":"https:\/\/pachterlab.github.io\/kallisto\/releases\/2015\/06\/09\/v0.42.2","guid":"https:\/\/pachterlab.github.io\/kallisto\/releases\/2015\/06\/09\/v0.42.2","pubDate":"2015-06-09T00:00:00+00:00"},{"title":"V0.42.1","description":"\n
index<\/code>\n \n
quant<\/code>\n \n
--single<\/code> flag to specify single-end reads<\/li>\n